chr15-26178900-C-T

Variant names:

• chr15-26178900-C-T
• rs547843

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0381 in 151,876 control chromosomes in the GnomAD database, including 153 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.038 (153 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0572 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0382 AC: 5792 AN: 151758 Hom.: 153 Cov.: 31

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0793

Gnomad AMR AF: 0.0300

Gnomad ASJ AF: 0.0756

Gnomad EAS AF: 0.000390

Gnomad SAS AF: 0.0206

Gnomad FIN AF: 0.0380

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0587

Gnomad OTH AF: 0.0373

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0381 AC: 5789 AN: 151876 Hom.: 153 Cov.: 31 AF XY: 0.0360 AC XY: 2675 AN XY: 74220

African (AFR) AF: 0.0102 AC: 424 AN: 41438

American (AMR) AF: 0.0299 AC: 456 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0756 AC: 262 AN: 3466

East Asian (EAS) AF: 0.000391 AC: 2 AN: 5114

South Asian (SAS) AF: 0.0206 AC: 99 AN: 4808

European-Finnish (FIN) AF: 0.0380 AC: 400 AN: 10536

Middle Eastern (MID) AF: 0.0240 AC: 7 AN: 292

European-Non Finnish (NFE) AF: 0.0587 AC: 3989 AN: 67934

Other (OTH) AF: 0.0369 AC: 78 AN: 2112

Alfa AF: 0.0257 Hom.: 155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.92
PhyloP100		-0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs547843; hg19: chr15-26424047;